I'm developing a functional annotation pipeline, and I'd like to use some methods that require a structural prediction. This needs to process several bacterial genomes a day, so if I want to run this on a single computer, I can only afford to take about 1 second per structural prediction. If I use our computational grid, I can take up to about a minute of CPU time per protein. If I limit myself to working on proteins with no annotation from another source, I can take several minutes of CPU time per protein.

Are there any open-source programs that can give me a 3D structural prediction, even if it's crude and inaccurate, in a few minutes per protein?